Service tax return filing related query

Please help me and give suggetion ;-

As our client providing taxable Service and cross the limit of Rs 10 lac in 31.03.2012.

Inform us in the month of August 2012 , as we are the new auditor and the previous auditor qualified their report by menationing the liability of service tax registration and service tax.

We apply for registration in service tax department in the month of august after introducing nagative list applicable from 1st July 2012 and got registered under other then nagative list.

We calculated the service tax  by utilizing the credit for the period ended march 2012 and paid the same.

Now we want to file the return for the period ended 31.03.2012 and the first quarter April-June 2012. 

But due to registration under the category of nagative list we are not able to file the return for the above period .........so please give us best suggestion.

for further clearification you can ask by email on camominsaifi @ gmail.com